- BioC+GitHub
15258(https://www.rdocumentation.org/)

15258
(https://www.rdocumentation.org/)









Multiple pieces of software used

Complete pipeline


Rcpp, not always ported to Rcpp

\[ Y_{iv} = X_{i} \beta_{iv} + Z_{i}\theta_{iv} + \varepsilon_{iv} \\ \varepsilon_{iv} \sim N(0, \Sigma_{iv}) \\ \Sigma_{iv} \sim \text{AR} \]
\(Z_{i}\) can be different for each \(i\) (scrubbing), but usually isn’t.
voxel package

preprocessfMRI from ANTsRspm12r - https://neuroconductor.org/neuroc-help-fmri-analysis-spm12rfslr - https://neuroconductor.org/neuroc-help-fmri-analysis-fslrhttps://grand-challenge.org/all_challenges/

ANTsR/extrantsr
antsRegistration - rigid/affine/non-linear diffeomorphicextrantsr::registration - wraps antsRegistration to use nifti objectsfslr
flirt - linear/affine registrationfnirt - non-linear registration (need affine first)fnirt_with_affine - wraps above 2
registration from extrantsr is a general function to do linear/non-linear registration, using antsRegistration
EveTemplate/MNITemplate - templateskirby21 seriessri24 - SRI24 MRI Atlasmalf.templates - templates for label fusionneurohcp - download data from HCP/INDInitrcbot - download data from NITRCneurovault - download data from https://neurovault.org/EBImage - image processing and analysismagick - Bindings to ImageMagickswarm-lab/ROpenCVLite or ropenscilabs/opencvoro.dicom - read/write DICOM datadcm2niir - uses dcm2niix from Chris Rordendivest - Rcpp wrapped dcm2niixdcmtk - interface package for DCMTKmatlabr - could use dicomread MATLAB code and excecute through R